DNA sequencing has seen dramatic cost reductions in recent years, while sample preparation costs have been relatively flat. The result is a `sample preparation bottleneck' apparent today will affect essentially all sequencing studies within a few years. In addition, sample input quantity requirements for standard approaches exclude important low-yield clinical sample types. The goal of this R21 project is to validate and demonstrate a practical integrated microfluidic sample preparation technology for pathogen genome sequencing that enables a significant advance in sample preparation cost, turn-around-time, and low-input capability. Integration of the entire sample preparation process in a single micro device will reduce real-world cost for high-throughput sample preparation more than 10-fold by lowering reagent consumption, the need for other consumables, capital equipment costs, hands-on time, and procedural errors. We will validate this technology on S. Aureus samples from an ongoing clinical trial, Project CLEAR, and then go on to sequence a large number of additional Project CLEAR samples.